PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
1TZH
Biol. Unit 1
Info
Asym.Unit (173 KB)
Biol.Unit 1 (165 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE FAB YADS1 COMPLEXED WITH H-VEGF
Authors
:
F. A. Fellouse, C. Wiesmann, S. S. Sidhu
Date
:
09 Jul 04 (Deposition) - 31 Aug 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,H,L,V,W
Biol. Unit 1: A,B,H,L,V,W (1x)
Keywords
:
Phage Display, Antibody Library, Protein Engineering, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. A. Fellouse, C. Wiesmann, S. S. Sidhu
Synthetic Antibodies From A Four-Amino-Acid Code: A Dominan Role For Tyrosine In Antigen Recognition
Proc. Natl. Acad. Sci. Usa V. 101 12467 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PDGF_1 (V:49-61,W:49-61)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDGF_1
PS00249
Platelet-derived growth factor (PDGF) family signature.
VEGFA_HUMAN
75-87
2
V:49-61
W:49-61
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d1tzhb2 (B:114-213)
1b: SCOP_d1tzhh2 (H:114-213)
2a: SCOP_d1tzha2 (A:108-211)
2b: SCOP_d1tzhl2 (L:108-211)
3a: SCOP_d1tzhb1 (B:1-113)
3b: SCOP_d1tzhh1 (H:1-113)
4a: SCOP_d1tzha1 (A:1-107)
4b: SCOP_d1tzhl1 (L:1-107)
5a: SCOP_d1tzhv_ (V:)
5b: SCOP_d1tzhw_ (W:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Human (Homo sapiens) [TaxId: 9606]
(179)
1a
d1tzhb2
B:114-213
1b
d1tzhh2
H:114-213
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1tzha2
A:108-211
2b
d1tzhl2
L:108-211
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Engineered (including hybrid species)
(68)
3a
d1tzhb1
B:1-113
3b
d1tzhh1
H:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Engineered (including hybrid species)
(61)
4a
d1tzha1
A:1-107
4b
d1tzhl1
L:1-107
Class
:
Small proteins
(3458)
Fold
:
Cystine-knot cytokines
(124)
Superfamily
:
Cystine-knot cytokines
(124)
Family
:
Platelet-derived growth factor-like
(26)
Protein domain
:
Vascular endothelial growth factor, VEGF
(18)
Human (Homo sapiens) [TaxId: 9606]
(16)
5a
d1tzhv_
V:
5b
d1tzhw_
W:
[
close SCOP info
]
CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_1tzhV00 (V:14-107)
1b: CATH_1tzhW00 (W:14-107)
2a: CATH_1tzhA02 (A:109-211)
2b: CATH_1tzhB02 (B:114-213)
2c: CATH_1tzhH02 (H:114-213)
2d: CATH_1tzhB01 (B:1-113)
2e: CATH_1tzhH01 (H:1-113)
2f: CATH_1tzhL02 (L:109-211)
2g: CATH_1tzhA01 (A:1-108)
2h: CATH_1tzhL01 (L:1-108)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Cystine Knot Cytokines, subunit B
(102)
Homologous Superfamily
:
Cystine-knot cytokines
(102)
Human (Homo sapiens)
(84)
1a
1tzhV00
V:14-107
1b
1tzhW00
W:14-107
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1tzhA02
A:109-211
2b
1tzhB02
B:114-213
2c
1tzhH02
H:114-213
2d
1tzhB01
B:1-113
2e
1tzhH01
H:1-113
2f
1tzhL02
L:109-211
2g
1tzhA01
A:1-108
2h
1tzhL01
L:1-108
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDGF_1tzhW01 (W:26-104)
1b: PFAM_PDGF_1tzhW02 (W:26-104)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cystine-knot
(56)
Family
:
PDGF
(19)
Homo sapiens (Human)
(17)
1a
PDGF-1tzhW01
W:26-104
1b
PDGF-1tzhW02
W:26-104
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain H
Chain L
Chain V
Chain W
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (173 KB)
Header - Asym.Unit
Biol.Unit 1 (165 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1TZH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
